Conventional methods for manufacturing nanostructures with nanoscale precision such as dip-pen lithography and electron beam lithography require purpose-built lithography-only instruments and require various different custom built materials such as masks, resists, and patterns. Even with such conventional processes that require customized and expensive equipment, it is difficult to achieve molecular level precision in the generated nanostructures. Furthermore, imaging and characterizing such nanostructures often requires use of different equipment. There is a need for manufacturing and characterizing nanostructures built with nanometer scale precision in the same equipment.